Contacts of the strand formed by residues 128 - 133 (chain E) in PDB entry 1FV1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 128 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ILE* 1.3 78.5 - - - +
129E VAL* 1.3 64.0 + - - +
130E ARG* 4.2 27.0 - - + +
174E GLN 3.5 1.6 - - - +
175E VAL* 3.3 3.8 - - - -
176E GLU* 2.8 57.0 + - + +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E CYS* 4.3 3.4 - - - -
119E VAL* 3.6 24.5 - - + -
127E ILE* 4.5 8.0 - - + +
128E GLU* 1.3 79.7 + - - +
130E ARG* 1.3 70.0 + - - +
142E VAL* 5.9 0.7 - - - +
157E THR* 4.5 13.5 - - + -
159E VAL* 3.6 38.1 - - + +
173E CYS* 3.5 28.9 - - - -
174E GLN 3.4 2.5 - - - +
175E VAL* 3.9 11.2 - - + -
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Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLU* 4.4 22.5 - - + +
129E VAL* 1.3 85.9 - - - +
131E TRP* 1.3 65.1 + - - +
132E PHE* 3.9 28.8 - - + -
137E GLU* 3.2 34.0 + - - +
142E VAL* 6.5 0.2 - - - -
172E THR 3.6 0.7 - - - +
173E CYS* 3.4 3.3 - - - -
174E GLN* 2.7 54.0 + - - +
176E GLU* 5.1 15.0 + - + +
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Residues in contact with TRP 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 3.7 29.8 - - + -
115E LEU* 4.0 22.4 - - + -
117E CYS* 3.4 31.4 - - + +
130E ARG* 1.3 73.8 - - - +
132E PHE* 1.3 64.2 + - - +
137E GLU* 2.9 29.5 - - - +
138E GLU* 2.9 18.1 + - + +
142E VAL* 4.1 11.6 - - + +
159E VAL* 3.1 42.0 + - + +
161E LEU* 3.6 40.2 - - + +
171E TYR* 4.2 22.2 - - + -
172E THR 3.4 14.1 - - - -
173E CYS* 4.0 15.7 - - + -
186E VAL 5.3 0.4 - - - -
188E TRP* 5.4 0.2 - - + -
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Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG* 3.9 41.1 - - + -
131E TRP* 1.3 77.9 - - - +
133E ARG* 1.3 60.1 + - - +
134E ASN 3.2 7.1 + - - -
135E SER* 4.2 10.5 - - - +
136E GLN* 3.6 13.2 - - - +
137E GLU* 3.0 48.0 - - + -
170E VAL 3.7 0.5 - - - +
171E TYR* 3.4 4.1 - - - -
172E THR* 2.7 50.2 + - + +
174E GLN* 3.3 31.9 - - + -
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Residues in contact with ARG 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E TRP 4.3 0.4 - - - -
132E PHE* 1.3 67.4 - - - +
134E ASN* 1.3 57.3 + - - +
135E SER 3.3 6.9 + - - -
136E GLN* 3.0 25.5 + - + +
138E GLU* 4.4 17.5 - - + +
140E ALA 5.6 0.6 + - - -
161E LEU* 4.2 8.1 - - - +
162E GLU 3.9 8.7 + - - -
163E THR* 3.6 29.3 - - - +
164E VAL* 5.3 3.2 - - - +
169E GLU* 3.3 30.0 + - + +
170E VAL 4.3 4.3 - - - +
171E TYR* 3.2 33.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il